Installation

Preparation

• install mamba (a fast reimplement of conda)

conda install mamba -n base -c conda-forge

• Python environment

# linux
mamba env create -f build/scrna-recom_linux-64.yaml -n scrna-recom
# mac osx-64
mamba env create -f build/scrna-recom_osx-64.yaml -n scrna-recom

• R environment

# install R packages to scrna-recom environment
mamba activate scrna-recom
Rscript  build/install-r-pkgs.R

scrnaRecom

# install
remotes::install_github("WXlab-NJMU/scrna-recom", subdir="scrna-recom")
# uninstall
remove.packages("scrnaRecom")

Excutable commands are available under the scrnaRecom/exec folder after installation. That could be one of the followings:

• $HOME/miniconda3/envs/scrna-recom/lib/R/library/scrnaRecom/exec (install under scrna-recom environment)
• $HOME/R/x86_64-pc-linux-gnu-library/4.0 (local installation in Linux)

Please add that to PATH

pyscrnarecom

# install
git clone [email protected]:WXlab-NJMU/scrna-recom.git
cd scrna-recom && python setup.py install
# uninstall
pip uninstall pyscrnarecom

Excutable commands are available under the current environment.